Beta diversity

Between-sample variability from 16S rRna-gene sequencing data.

Clustering

PCA

Clustering by timepoint (PCA):

Clustering by treatment (PCA)

MDS

Clustering by treatment (MDS): NMDS1 vs NMDS2

## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.
## Warning: Removed 8 rows containing missing values (geom_point).

## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.

## Warning: Removed 8 rows containing missing values (geom_point).

Clustering by timepoint (MDS):

NMDS1 vs NMDS2

## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.
## Warning: Removed 8 rows containing missing values (geom_point).

Clustering by type (MDS): NMDS1 vs NMDS3

## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.
## Warning: Removed 8 rows containing missing values (geom_point).

Clustering by type (MDS): NMDS2 vs NMDS3

## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.
## Warning: Removed 8 rows containing missing values (geom_point).

Clustering by treatment by timepoint (MDS):

## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.
## Warning: Removed 8 rows containing missing values (geom_point).

## Warning: The shape palette can deal with a maximum of 6 discrete values because
## more than 6 becomes difficult to discriminate; you have 7. Consider
## specifying shapes manually if you must have them.

## Warning: Removed 8 rows containing missing values (geom_point).

Significance of between-group distances

Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.

Below the ANOVA table from the model:

\[ X = \mu + treatment + timepoint + treatment*type + e \]

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
treatment 6 0.6626034 0.1104339 1.020722 0.1197929 0.417
residuals 45 4.8686352 0.1081919 NA 0.8802071 NA
total 51 5.5312386 NA NA 1.0000000 NA

going 3D

## Run 0 stress 0.04298657 
## Run 1 stress 0.04235479 
## ... New best solution
## ... Procrustes: rmse 0.01071419  max resid 0.03832133 
## Run 2 stress 0.04369622 
## Run 3 stress 0.04373229 
## Run 4 stress 0.04366829 
## Run 5 stress 0.04241816 
## ... Procrustes: rmse 0.006091945  max resid 0.03044901 
## Run 6 stress 0.04235371 
## ... New best solution
## ... Procrustes: rmse 0.01041482  max resid 0.05778179 
## Run 7 stress 0.04236088 
## ... Procrustes: rmse 0.01017229  max resid 0.05697562 
## Run 8 stress 0.04240378 
## ... Procrustes: rmse 0.007020887  max resid 0.03974594 
## Run 9 stress 0.04364633 
## Run 10 stress 0.04560874 
## Run 11 stress 0.04356367 
## Run 12 stress 0.04365055 
## Run 13 stress 0.05413756 
## Run 14 stress 0.04921116 
## Run 15 stress 0.04243655 
## ... Procrustes: rmse 0.007022739  max resid 0.03948807 
## Run 16 stress 0.0423677 
## ... Procrustes: rmse 0.01022542  max resid 0.05746601 
## Run 17 stress 0.04249901 
## ... Procrustes: rmse 0.01121507  max resid 0.06154593 
## Run 18 stress 0.04927696 
## Run 19 stress 0.04560166 
## Run 20 stress 0.04918369 
## *** No convergence -- monoMDS stopping criteria:
##     19: no. of iterations >= maxit
##      1: stress ratio > sratmax

Treatment AE1

timepoint 8

treatment Carvacrol

treatment p-cymene

treatment γ-terpinene

treatment 0

treatment “”